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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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java.lang.ArithmeticException: / by zero #84

Closed MichelMoser closed 5 years ago

MichelMoser commented 5 years ago

Dear Pilon developers,

When running pilon on some medaka output, i get following error:

Exception in thread "main" java.lang.ArithmeticException: / by zero at org.broadinstitute.pilon.GenomeFile.contigRegions(GenomeFile.scala:71) at org.broadinstitute.pilon.GenomeFile.$anonfun$regions$1(GenomeFile.scala:53) at scala.collection.immutable.List.map(List.scala:286) at org.broadinstitute.pilon.GenomeFile.(GenomeFile.scala:53) at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:102) at org.broadinstitute.pilon.Pilon.main(Pilon.scala)

I checked for contigs with length 0 but shortest contig in assembly is 4 bases. It it creating the error?

Thanks, Michel

MichelMoser commented 5 years ago

Sorry, there was a 0 length contig in there. Just spotted it too late =)